ANNOUNCE: GCUA - General Codon Usage Analysis
This program is designed to calculate various parameters that might be
relevant in accessing the codon usage patterns of a group of genes.
The most relevant features of this program include:
- A Clustal-like menu interface
- Reads FASTA-formatted files
- Multivariate analyses of codon usage (RSCU) and amino acid patterns
(Principle components, sum of squares and cross products,
correspondence analysis, correlation analysis)
- Calculation of codon usage frequency
- Calculation of RSCU values
- Calculation of amino acid frequency data
- Calculation of base composition
(GC1, GC2, GC3, GC3s)
- Calculation of distances between genes, based on RSCU values
(PAUP and PHYLIP-compatible)
- Output in spreadsheet-readable format
(Cricket Graph or MS Excel)
- Online help available
- Can be used in conjunction with the ADE package
- Universal and Mycoplasma/Spiroplasma code supported
- Ability to analyse complete prokaryotic genomes
(up to 5,000 genes each with a maximum length of 15,000 bp)
- Incredibly poor documentation
- Silly name
The program is available from:
ftp://ftp.nhm.ac.uk/pub/gcua/
in either tarred/compressed fromat for SUNOS or in stuffit/binhex format
for PowerMAC.
In the not-too-distant future, I hope to add more executibles to the
server (IBM, DEC, SGI, VMS, 68K mac). Maybe if there is some demand, it
might get me to do it.
The goal of this program was to provide an easy-to-use method (for free)
of analysing codon usage in complete prokaryotic genomes. The user can
look at codon usage (or any other statistic) in the dataset as a whole
or for each gene individually. Variation in codon usage can be examined
either by looking at distances between the genes based on their codon
usage, or using multivariate analysis techniques (the user should get to
know a little of the philosophies/methods of multivariate analyses
before attempting this).
The software is distributed without any warranty/guarantee/decent
documentation. It should also be treated as beta software. Although
the results, so far, seem to be fairly consistent, I cannot and will not
guarantee that it will do anything. Use as you will, report bugs if you
can and let me know of any problems. Also, send me an email if you
download the software and decide to use it (for update info etc.).
Question: Why am I not releasing the code?
Answer: 'Cos it is embarassingly poor at the moment, but when I've
tidied it up a bit, I might make it available.
Comments and suggestions are particularly welcome.
regards,
James
--
=========
James O. McInerney email: J.mcinerney@nhm.ac.uk
Senior Scientific Officer, phone: +44 171 938 9247
Department of Zoology, Fax: +44 171 938 9158
The Natural History Museum,
Cromwell Road,
London SW7 5BD.
=========
This directory contains:
======== Documents =============
READ.ME This file
gcuadoc.rtf Rich Text Format documentation for the program
(can be read by MS Word).
======== Software ==============
gcua.DEC.tar.Z Program compiled for DEC alpha (tarred and compressed).
gcua.IRIX.tar.Z Program compiled for IRIX (tarred and compressed).
gcua.MacOS.sit.hqx Program compiled for powermac (stuffed and binhexed).
gcua.sun.tar.Z Program compiled for SunOS (tarred and compressed).
gcua.linux.tar.Z Program compiled for linux (tarred and compressed).
======== Test data =============
GMG.seq The Mycoplasma genitalium genome, sequenced at The Institute
for Genomic Research (TIGR: http://www.tigr.org).
This genome has a very interesting and unique
codon usage pattern, see: McInerney, J.O., 1997; Prokaryotic
Genome Evolution as assessed by Multivariate Analysis
of Codon Usage Patterns. Microbial and Comparative Genomics
2(1), 1-10.
======== Other ================
Putgaps Directory containing a program (and source code)
for putting gaps in DNA sequences according to where
they appear in a file of aligned protein sequences.
Translfas Directory containing a program (and source code)
for translating a file of DNA sequences into their
protein equivalents. All of the genetic codes
are supported.
===============================